The aim of this study was to validate two separation methods for determination of inorganic anions and cations from natural waters with capillary electrophoresis (CE) by using indirect-UV detection. The research is related to method development for screening of groundwater samples obtained in site investigations for spent fuel of the Finnish nuclear industry. In CE analysis, anions were separated in pyromellitic acid (pH 7.7) in the order bromide, chloride, sulphate, nitrite, nitrate, fluoride and dihydrogenphosphate. Cations were separated at pH 3.6 after anions using an 18-crown-6-ether solution. In these analyses, ammonium migrated first followed by potassium, calcium, sodium and magnesium. The concentrations of the ions in the natural water samples were calculated by using two or three calibration curves made using reference solutions at concentration levels of 0.5–250 mg/l. The repeatabilities of the anion and cation methods were tested using laboratory-made reference sample mixtures with high and low salt concentrations. The limits of quantification in the analyses were between 0.02 and 0.1 mg/l, depending on the ion. Concentrations of ions tested in natural waters varied from a few milligrams to tens of grams per litre.